[GSoC] weekly report #9

[Artem Tarasov]

Hello everybody,

My progress report for the past week is available at
http://lomereiter.wordpress.com/2012/07/17/gsoc-weekly-report-9/

I've implemented sorting and merging, both parallelized and quite fast.
Also my merging tool improves on ideas taken from Picard source code and
merges SAM headers as well as sorted alignment records.

For those who use Debian, packages for amd64 and i386 are now available:

https://github.com/lomereiter/sambamba/downloads

At the moment, alternatives to the following samtools commands are
developed: view, index, sort, merge, flagstat. The current limitation is
that most tools don't work with stdin/stdout and work with BAM files only
(does anybody still use SAM?). Nevertheless, they wisely use multi-core
processors and usually give a better speed.